Thursday 30 July 2009 20.43 EDT
First published on Thursday 30 July 2009 20.43 EDT

Troops were last night on a door to door hunt for Islamist militants after government forces stormed the base of a self-styled Taliban leader and killed him and more than 100 rebels in an attempt to crush an uprising that has racked Nigeria.

A local rights group accused security forces of killing unarmed captives alleged to be members of the radical Boko Haram sect seeking to overthrow the government and impose sharia law across Nigeria.

A bystander in Maiduguri, northern Nigeria, told the BBC he saw three men shot dead at close range while they were kneeling on the floor with their arms in the air.

The army insisted that it had used only minimal force, arguing that the alleged sect members were armed with machine guns and rocket-propelled grenades.

However, officials last night said the sect leader, Mohammed Yusuf, had been shot and killed in police custody.

The police commander of Borno state said on state radio that Yusuf had "died in police custody". He gave no further explanation, but the state governor's spokesman, Usman Ciroma, told the Associated Press: "I saw his body at police headquarters. I believe he was shot while he was trying to escape."

Shamaki Gad Peter, director of the League for Human Rights, said rights workers saw up to 20 people dead after the start of the government offensive on Wednesday. There had been no weapons on the bodies, he said, and some people appeared to have been shot from behind, suggesting they were escaping.

Linda Dukwa, a resident of Maiduguri, said she and her family had been hiding in terror after police killed two men in front of her on Monday. "They were dressed in white robes," she said, indicating they were sect members. "They were held by policemen. Then they shot their feet. After they fell on the ground [the police] shot their heads."

About 5,000 people have reportedly fled the city. But Ali Modu Sheriff, governor of Borno state, of which Maiduguri is the capital, said the militants had been dislodged and urged people to go about their normal business. "The house-to-house search is still going on and anybody that harbours them will be dealt with according to the law," he said on state radio.

Yusuf had initially escaped capture along with about 300 followers but was caught last night, according to the state police commissioner, Christopher Dega.

Earlier, an AP reporter watched soldiers shoot their way into the mosque in Maiduguri and rake those inside with machine gun fire. The reporter later counted about 50 bodies inside the building and 50 in the courtyard. The militants, armed with hunting rifles, bows and arrows and scimitars, proved no match for government forces and some fled. Another five corpses lay inside a nearby house. The army commander, Major General Saleh Maina, pointed to the body of a plump, bearded man, saying it was Boko Haram's vice-chairman, Bukar Shekau. "The mission has been accomplished," he said.

In the violence that began on Sunday in Borno, Islamist militants attacked police stations, churches, prisons and government buildings. The violence quickly spread to three other states in mainly Muslim north Nigeria. Yesterday, men in Bauchi state and Maiduguri trimmed and even shaved off their beards in an effort to avoid being targets for the security forces.

Umaru Yar'Adua, Nigeria's president, said the sect was preparing "holy war". Security agents had been watching the group for months and the order to attack came when the movement began gathering fighters from nearby states, he said.